Pokemon XD 2: Darkening Skies
by sceptile8308
Summary: Cipher has returned to Orre and Ash & Co. as well as Team Rocket are off to Orre to stop them. Will they succeed or is Cipher's power to great for them?
1. To Orre

Pokémon XD 2: Darkening Skies

Chapter 1: To Orre

Today, we find our heroes in Pallet Town, just after Ash had finished the Sinnoh League. Professor Oak and Ash's mom are throwing another huge party.

"Congratulations on doing so well Ash," said Delia, "and for bringing home another trophy."

"Thanks Mom," Ash replied.

The party was being held at the Oak Ranch and it seemed as though all of Pallet was there. There was lots of food, and many Pokémon. Dawn was impressed with the size of the party.

"This party is amazing. Who thought that a small town could throw such a big party," said Dawn.

Brock replied, "After the third, you get used to it."

Dawn then noticed all the pokémon. There was a Muk, Bayleaf, Totodile, Cyndaquil, Bulbasaur, Noctowl, Heracross, Kingler, Sceptile, Glalie, Torkoal, Swellow, Donphan, Corphish, and Snorlax as well as Ash's Staraptor, Buizel, Monferno, Grotle, and Pikachu. "Who are all these pokémon?" she asked.

"They are all Ash's. Some from Kanto, the Orange Islands, Johto, Hoenn, and Sinnoh, Brock told her, "Although some are not here."

"Who?" Dawn asked. Her questioned was partly answered when the ground began to quake. People began to shout "Stampede!" and run, leaving Ash alone right in the way of a herd of Tauros. Ash just stood there, glaring at the Tauros. Dawn could not figure out why Ash was not running.

Suddenly, Ash called out, "STOP!" in a commanding voice making all the Tauros halt immediately. Dawn asked Brock, "Why did they all stop?"

"All 30 of those Tauros are Ash's." he replied. "He also has a Charizard, Squirtle, Lapras, Pidgeot, Primeape, and Butterfree."

"Wow, I never knew he had that many," said Dawn.

A while later, once the party was back in full swing, Tracy came out and told Prof. Oak something which caused him to go inside the lab. After the party was over, Prof. Oak asked Ash to come to his lab. When Ash, Dawn, and Brock arrived, they saw the Professor was looking upset about something. "What's the problem Professor?" they asked.

"I have a colleague in the Orre region named Prof. Krane," he told them, "and he has just called and given me some rather disturbing news. He said that shadow pokémon were being reported in Orre again."

"Shadow pokémon?" they said quizzically.

"They are pokémon who's hearts have been closed to make them more powerful. Both times they have appeared in the past, it was because of an evil organization called Team Cipher." Oak told them.

"NOT THEM AGAIN!" said 3 unknown voices.

"Who's there?" asked Prof. Oak.

Suddenly Team Rocket came out and started to do their motto, but was cut off when Prof. Oak asked them what they knew of Team Cipher.

James replied, "Team Rocket was once asked by Cipher to help them accomplish world domination through shadow pokémon."

"But our boss said shadow pokémon were horrible creations and would not help them," Jessie continued.

"It was either because he thought it was cruel, or he didn't like the fact that once a pokémon became shadow that it would then stop growing stronger." Meowth finished.

"However we believe in the first option," said Jessie.

Prof. Oak then questioned Team Rocket about Cipher and Ash and Co. listened closely. They all learned about the first two shadow incidents, the first 10 years ago and the second five years ago. Ash, Brock, Dawn, as well as Team Rocket, which surprised everyone present.

"What, we hate the idea of closing the door to a pokémon's heart," said James.

"I'm not exactly fond of it either," Meowth said dryly.

"Then it's settled," said Brock, "We will have a temporary truce as we go to Orre and remove Cipher." Everyone agreed to this and prepared to go, agreeing to meet back in two days to head for Orre. Ash, and Brock then proceeded to make some calls, and Dawn asked Prof. Oak what they were doing.

"They are calling people to have their other team members sent to them," The pokémon professor said, "Most of Brock's are at the Pewter City Gym I believe, and Ash has many pokémon elsewhere."

"Oh yeah, I forgot that," said Dawn. A little while later they went to the Ketchum residence for the night, and Ash told his Mom what their plans were.

"Oh my gosh, I can't believe people would close a pokémon's heart just to make them stronger!" she cried in disbelief, "You better make sure you take them out dear."

"I will do whatever I can to stop them," replied Ash. Then they all went to bed for the night to get ready for the challenges ahead.

- - -

Two days later, Ash, Dawn, and Brock met with Jessie, James, and Meowth to begin their journey to Orre. Each person brought their strongest and most trusted team. It was a long boat ride to Orre. First, they had to take a small ferry from Pallet to Vermillion, before boarding a larger boat headed to Olivine, and then a final ship to Orre.


	2. Ambush

**-I don't own pokémon.**

Pokémon XD 2: Darkening Skies

Chapter 2: Ambush

Ash and Co. have reached Olivine and are boarding the S.S. Silver to Gateon Port in Orre. After they reached Orre, they would head to the Pokémon HQ Lab to see what they could do to stop Cipher. They boarded the ship and headed to the deck to watch for some leisure time when a voice came over the ship's PA.

"This is your captain speaking. We have just departed from Olivine City and will arrive at Gateon Port around 8:00am tomorrow morning. Please enjoy your stay on the S.S. Silver."

"I can't wait to get to Orre," Ash said, "I am soooo bored."

"I know, let's have our pokémon come out and enjoy the boat," Brock said.

So, everyone sent out their pokémon. Brock sent out Swampert, Steelix, Crobat, Sudowoodo, Ludicolo, and Geodude. Dawn sent out Pachirisu, Mamoswine, Buneary, and Piplup. Jessie sent out Seviper, Wobuffet, and Yanmega. James sent out Carnivine, Mime Jr., and Cacnea (Gardenia gave it back to James when they passed through Eterna City on their way to Twinleaf Town after the Sinnoh League). Ash sent out his team of Pidgeot (yes, he finally went back and recaptured him), Snorlax, Charizard, Sceptile, and Donphan. Pikachu and Meowth were already enjoying the breeze on the front of the ship and all the other pokémon soon ended up there as well. As the pokémon started to play and enjoy themselves, Ash, Brock, Dawn, Jessie, and James began to explore the rest of the ship.

- - -

That night everyone was asleep in their rooms. Everyone decided to let their pokémon sleep outside of their pokéballs. Around 10:00pm, the ship jolted and shook, waking up all the passengers. Ash and Co. (now includes Jessie and James) ran out of their rooms and onto the deck with everyone else.

Their they saw two helicopters with grappling hooks attached to the S.S. Silver. A third copter landed on the front deck of the ship. Out stepped several people in weird white costumes (the Cipher Grunt where from Gale of Darkness). One of them, the leader presumably, started issuing orders to the grunts. The grunts then proceeded to throw the life boats into the water, then the passengers.

Jessie and James immediately recognized Cipher so Ash and Co. leapt into action. Ash ran for copter while the others attacked the grunts. Suddenly, an explosion came from behind as the interior of the ship was bombarded with bombs filled with sleeping gas. Ash reached down to his belt to grab a pokéball, but then remembered that they were all empty, the pokémon were still inside the ship. The grunts were returning to the copter and Ash realized that he was the only one who was not already overboard. He climbed into the empty copter and hid in a small storage closet. Inside he found a box with what seemed to be pokéballs and another small box. The copter started to come to and Ash listened to the grunts' conversation.

"That's everyone," the first grunt said, "let's get the snag balls out of the closet and capture those pokémon before we sink this ship."

Ash guessed that they were coming to his closet, so he quickly pocketed the box, and what he assumed were two snag balls before the door came open.

"Hey, you get out of here," the grunt said. He then grabbed Ash and threw him out of the copter and all the way off the ship.

As Ash hit the water he realized all his pokémon were still on the ship, including Pikachu. He resurfaced and began swimming towards the boat as quickly as he could. A few moments later, he saw the copter take off before a dark colored beam hit the ship. Ash suddenly realized what had happened. Those Ciphers had stolen all the pokémon on the ship.

"PIKACHU!" Ash screamed, and was surprised when he heard a reply.

"ASH!" he heard and turned to see the rest of the gang in a small lifeboat coming towards him. He also saw two people he did not recognize. After he was dragged into the boat, he was given one of the emergency blankets and told to sit down. Then he was introduced to the two unfamiliar people.

"Ash, this is Captain Richard and his first mate Mendelson," Brock said, but Ash was not listening because he was sobbing about the loss of his pokémon and friends, especially Pikachu. Dawn saw this and sat down next to Ash and began to comfort him and ask what was wrong.

"Pi-pikachu," Ash said weakly and Dawn assumed that all the pokémon had still been on the boat.

"No, they can't be…" was all she could say.

"No," Ash replied, "They aren't dead. Cipher captured them all before destroying the ship."

"Don't worry Ash, will get them back," Brock said reassuringly, "we always have before." However, everyone still cried for their captured and imprisoned pokémon as they slowly rowed towards Gateon Port for the rest for the night.


	3. Gearing Up

**Here is chapter three. Please enjoy.**

**Also, please review, this is my first fic and would like to know how I am doing.**

**Disclaimer: I don't own pokémon.**

Pokémon XD 2: Darkening Skies

Chapter 3: Gearing Up

The following afternoon, the passengers of the S.S. Silver finally entered Gateon Port on a group of Coast Guard boats. About an hour and a half of waiting and no sign of the S.S. Silver, the Coast Guard had sent out patrol boats and found the passengers around noon and got them Gateon Port around 2:00pm. On the ride back, Ash and Co. explained to the Coast Guard the attack and theft of the pokémon by Cipher. Now they were arriving in Gateon Port where a large crowd waited to greet them.

Ash was still sulking about losing Pikachu. He could not believe that someone had not only stolen Pikachu, but actually got away. The group slumped towards the Pokémon Center, tired after the events of the previous night.

After spending the night at the Pokémon Center, Ash and Co. set out for Prof. Krane's Lab. Along the way, Brock began to notice that there were not any wild pokémon around. He pondered this for a while, but decided not to say anything to the rest of the group, they were depressed enough, so he would just wait and ask Prof. Krane.

Eventually the group saw a building through the trees. As they headed towards it, they realized it was the Pokémon HQ Lab. They were amazed at the design of the two story structure as they entered the clearing. As they began to head for the entrance, Brock heard what sounded like the cry of a young Pokémon. He looked around and finally spotted a pin with several young Eevee.

When Ash and Co. entered the lab, they were greeted by a young secretary. "Hello, are you the group sent by Prof. Oak?" she asked them.

Brock was about to pronounce his undying love for the woman, that is, if Jessie had not restrained him by grabbing his ear first. Dawn immediately confirmed that they were and asked if they could see Prof. Krane.

"Certainly," the young woman replied, "Just take the elevator up to the second floor, it's the first door on your right."

Upstairs, in Prof. Krane's office, a man in a white lab coat was talking to a woman who looked like she was in her mid-forties. She was wearing a pink shirt and matching knee length skirt with her hair tied above her head.

"I still can't believe the snag machine is beyond repair," the man in the lab coat remarked, "Without it, we can't stop cipher, and we don't have time to build another one!"

"Don't worry," the woman replied, "We will come up with something."

"I just wish that Kaminko was still here to help us," the man said. One year after the second attack by cipher, Prof. Kaminko had passed away due to heart failure. It had come as a shock to everyone at the lab.

"He was a good man, but there is nothing we can do about it now," the woman told him. Just then, there was a knock at the door. When the woman opened the door, she found Ash and co.

"Oh," she said, "You must be the group sent by Oak. My name is Lily, and this man here is Prof. Krane."

"Hi," replied Dawn as Jessie restrained Brock by the ear again, "I'm Dawn, and this is Ash, Brock Jessie, and James," she said as she introduced everybody.

"Ah, you finally made it," said the Prof. "I heard about the S.S. Silver and I am terribly sorry for your losses," Everyone hung there head at his words. "However, our job is to get them back, along with the other shadow pokémon. Unfortunately, the snag machine was destroyed, and a new one will take too much time to make."

"I think I may have a solution," Ash said. He then pulled out the two pokéballs and the box he had taken from Cipher's copter. "I heard one of the grunts refer to snag balls and I think that these are them." He then handed the snag balls to Prof. Krane. Krane put one of the snag balls under the scanner to look at it. The snag ball itself was red and white like a pokéball, but there was no latch and instead of one smooth center line, the two sides interlocked in a weaved fashion similar to a baseball.

"My scan shows that these were made from regular pokéballs, but with several added features," the Prof. told the group, "Besides being able to snag a trainers pokémon, they cannot catch wild pokémon and will not revert back to a normal pokéball unless there is a pokémon inside it. Also, they will genetically fuse with whoever touches the ball after a snag, and the pokémon inside will only obey that person. Even if it is traded, it will still only obey the master who grabbed the snag ball unless it is snagged again."

Everyone was surprised at the special qualities of the snag ball. Krane then said, "I may be able to use one of these to turn other pokéballs into snag balls. You guys take the other to see if you can capture a shadow pokémon." He then gave one of the snag balls back to Ash and kept the other.

Prof. Krane then proceeded to open the small box Ash had given him. Inside was what looked like another snag ball, except that it was purple and white. When he placed it under the scanner, the computer came up with nothing. It looked like it might take a while to solve the mystery of that snag ball.

That evening, Lily found everyone a place to sleep. Brock, Jessie, and James each used a guest room. Lily then took Ash and Dawn to two other rooms.

"These two rooms belong to my son and daughter, Michael and Jovi, who are on their own journey. I don't know when they will get back, but you two can use their rooms for now. Dawn, you take Jovi's room, and Ash can take Michael's room." She then left them to go to bed.

That night, all of the group had a restless night, for they all were worried about their pokémon, and how to get them back from Cipher.

**End of Chapter 3**

**I'm back and I am writing again. Yahoo!**

**Please enjoy. Cipher is back next chapter.**

**Please read and review.**


	4. Attack at HQ

**It is good to be working on this story again**

**I would like to know how I am doing, so please read and review**

**Disclaimer: I don't own Pokémon**

Pokémon XD 2: Darkening Skies

Chapter 4: Attack at HQ

The next morning, Ash and Co. woke up still very tired. They had very little sleep due to worry about their pokémon. Lily noticed their sad expressions at breakfast, so she decided to try and cheer them up.

"Today," she told them, "I will show you around the lab."

Her tour started outside the lab by the Eevees Brock had seen the day before.

"These Eevees," Lily told the group, "are all raised to act as starters for anyone in the area."

"Are any of them ready to be given out as a starter?" Brock asked.

"No," Lily replied, "but several almost are."

They then proceeded into the lab and entered a room with several workers and a Blissey. In the center of the room was a small pedestal with several glowing links connected to it.

"This is the purification chamber," Lily said, pointing to the pedestal, "When you stand on this pedestal, you are taken to a holographic world where you can move your pokémon here to be purified. Would someone like to test it?"

Dawn volunteered and stepped onto the platform. One of the technicians then activated the chamber. Nothing changed for the rest of the group, but Dawn suddenly had a vacant look because she was now seeing inside the purification chamber. Lily then signaled the technicians to bring her out, which they promptly did.

"In the chamber, you arrange four regular pokémon around a shadow pokémon," Lily explained, "It is best if the one that the shadow pokémon is facing is a type that it is strong against. Also the four regular pokémon stand in a circle facing the next. For the best result, each pokémon should be facing another that is a type that its own type is strong against."

They then went upstairs to a room with a similar pedestal.

"This is the battle sim system," said Lily, "You use this holographic system like the purification chamber, but in this system you are given a set team of pokémon to fight against a virtual trainer. Are there any volunteers?"

Ash immediately volunteered for this one. He stepped onto the pedestal.

"The battles are ranked one to 10 with 1 as the easiest and 10 the hardest. Which would you like?" Lily asked him.

"How about a level 7?" Ash told her. She nodded and began the sim.

Ash saw the world dissolve around him and a coliseum took form around him. He was then informed of his team, which consisted of 3 pokémon, via the virtual pokédex that appeared in his hand. Another trainer was on the other side of the field. The virtual ref then gave the rules.

"This will be a two-on-two double battle. When both pokémon on one side are unable to battle, then the other side wins. If both sides are ready, then BEGIN!"

Ash threw his first pokéball. "GO MAGMAR AND ELECTABUZZ!" he shouted. His opponent sent out a Vaporeon and Glaceon.

Ash made the first move, "Magmar, use flamethrower on Glaceon and Electabuzz use thunderbolt on Vaporeon."

"Vaporeon, block flamethrower with water gun, and Glaceon, block thunderbolt with ice beam and then use bubble and icy wind," Ash's opponent called.

Ash knew that both moves would hit both his pokémon, and both would lower their speed, so he called, "Electabuzz, Magmar use protect."

His two pokémon created green protective shields around themselves, preventing damage.

"Now use heat wave Magmar," Ash told the fire type. Magmar began to blow an extremely hot wind at his opponents. Vaporeon was not really bothered, but Glaceon was looking worse for wear.

"Now, Electabuzz hit Vaporeon with shockwave." Electabuzz quickly launched the undodgeable move. It hit Vaporeon, causing it to groan in pain.

His opponent then called, "Glaceon Vaporeon, double aurora beam on Electabuzz."

Ash countered by saying, "Electabuzz, Magmar block them with thunderbolt and flamethrower, then go into fire blast on Glaceon and thunder on Vaporeon."

Both of Ash's pokémon did as commanded and quickly blocked the aurora beams before launching the powerful attacks at the two Eevee evolutions causing a huge explosion. When the smoke cleared, it was obvious that neither of the virtual opponent's pokémon were going to get up.

The ref called it. "Neither Glaceon or Vaporeon are able to battle. Ash Ketchum is the winner!"

Ash cheered as the stadium faded away and the lab slowly reappeared to Ash.

"Awesome battle Ash," Lily said, "We all saw it on the monitor."

"Ash is definitely looking happier," Brock quietly said to Dawn.

"That's for sure," Dawn replied.

They left the battle sim room and headed back downstairs and entered Prof Krane's lab which was across the hall from the purification chamber. Prof. Krane was there waiting for them.

"Hello," he said, "welcome to my lab. I have some stuff here for you." He then grabbed one of several headbands off his desk. "This is an aura reader. It lets you know if the pokémon you are fighting is a shadow pokémon."

Just then, there was a large crash outside and everyone ran to check it out. Once outside, they saw that all the Eevees were in a cage and being loaded onto a truck by several cipher grunts.

"What are do you think you are doing with those Eevees?" Lily shouted at the Grunts.

"We are taking them to make them into shadow pokémon," one grunt replied, "and you won't be able to stop us."

Two more grunts joined them and they each through a pokéball. A Chikorita, Cyndaquil, and Totodile came out. They looked normal to everyone but Ash.

"Why do they have a dark aura?" Ash asked the Prof.

Prof. Krane put on the aura reader that he was still holding. "All three of them are shadow pokémon," he told the group.

The grunts were more worried about other things. "Target the boy in the hat first," the lead grunt told the other two, "He is too dangerous since he can see the shadow aura."

All three grunts then commanded there pokémon to use Shadow Blitz towards Ash. Ash had to quickly jump out of the way to avoid being hit. Since none of the group had their pokémon, they really were in trouble. The grunts then commanded Chikorita to use Shadow Razor, Cyndaquil to use Shadow Thrower, and Totodile to use Shadow Gun and all to attack Ash, but Shadow Razor hit Totodile, which made Shadow Gun hit Cyndaquil, thus causing Shadow Thrower to go wide.

"You idiots!" the lead grunt shouted at his companions. As the grunts bickered, Krane moved next to Ash.

"Ash, now's your chance, throw the snag ball," he told Ash.

Ash grabbed the snag ball and had to quickly decide which to get. He noticed Cyndaquil was close to the grunts and Chikorita had not been hit by an attack. That left Totodile, who seemed a little spaced from the Shadow Razor and was sitting closer to Ash and Co. then the grunts. Ash immediately took his chance and threw the ball at Totodile. Totodile did not even struggle, so the snag was easy.

This caused the grunts to pay attention. "Get that snag ball," the lead grunt commanded. However, as the other two grunts ran for the snag ball, they were hit by several golden stars.

The whole group looked and realized that one of the Eevees had launched the attack. While the grunts were distracted, Dawn quickly ran up and grabbed the snag ball. She instantly felt a warmth in her hand as the ball and the Totodile linked to her.

"Dawn, send out Totodile to fight back," Krane told her. Sawn sent Totodile out and told it to hit the Eevee cage with a Shadow Gun, while at the same time, the Eevee from earlier launched a Shadow Ball at the same spot. The two attacks caused the cage to bust, but the Eevees were cornered by the other grunts.

Then, out of nowhere, Brock charged and tackled the grunts, grabbed the Eevees, and headed for the lab.

"You better leave before we snag your other pokémon," James warned the grunts. This made the grunts quickly return Chikorita and Cyndaquil before they climbed in the truck and fled.

**Wow, that didn't take long**

**Thanks to everyone who has read**

**Please review, I know what Ash will get pokémon wise, but please give me ideas for the others**

**I hope the next chapter comes this quick**


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